CAUGHT IT!!! I went down to put the silkies to bed and thank goodness I went down a little earlier than planned since there was a very distinct black body half into the coop. I peaked through the window and a black snake was peaking right back at me. Thank goodness the more savvy birds were hiding at the back of the coop away from being snackables. I promptly returned the silkie to where it was safe and got my fiance. Together we managed to wrangle the 4 ft snake and then I drove it far away from my house. THAT was a nerve wracking drive. I love black snakes and have always been very careful not to hurt any when they bask on my driveway however, this one now viewed the coop as a food dispenser. So rather than kill it, I relocated it. The thing that just boggle my mind is that all grass near the coop is trimmed way down (to keep other predators away), there is no junk or easy hiding places since the coops are all stilted AND we have wire all around the run. This was one very lucky or determined snake to be able to get in. At least we now know what did kill my Powder Puff (*sniff*) and have to hope that other snakes will give the area a wide berth. They have also started integrating with the older flock and turkeys so there are older and wiser heads to protect them. 
Thanks for all the suggestions!